u/daro7
Contamination in microbiome blanks can come from neighboring samples, so blank detection alone cannot establish reagent origin, as [Minich and colleagues found](https://pubmed.ncbi.nlm.nih.gov/31239396/).
Contamination is most consequential near the low abundance and low prevalence edge of a biomarker list. The PubMed abstract reports fecal metagenomic sequencing and 696 species differing significantly between diarrheal and normal yaks, but it does not describe negative controls. A direct diagnostic is to compare each candidate’s prevalence and abundance in biological samples against extraction blanks, library blanks, and sequencing controls before interpreting group separation. Were those controls sequenced and analyzed with the same taxonomic pipeline, and which reported species remained above their control distributions?
Before interpreting the expanded diversity in GVMAGs V2, contamination and compositional context need to be visible. The catalogue contains 18,727 metagenome-assembled genomes, and alternative or custom genetic codes changed gene calling in more than 1,300 of them. A direct diagnostic would compare prevalence, coverage breadth, and normalized abundance against extraction blanks and library controls, using a stated denominator such as total reads, viral reads, or reads mapped to the catalogue. Which negative controls were processed through assembly and genome recovery, and do the rare lineages remain distinguishable from reagent or batch signals?
